Sodium in PDB 3fde: Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution

The structure of Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution, PDB code: 3fde was solved by H.Hashimoto, J.R.Horton, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.79 / 1.41
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	84.678, 103.691, 149.838, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.6

The binding sites of Sodium atom in the Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution (pdb code 3fde). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution, PDB code: 3fde:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na637 b:11.8 occ:1.00 O E:HOH115 3.1 18.7 1.0 N A:VAL451 3.1 10.9 1.0 O D:HOH211 3.2 17.4 1.0 N2 D:DG406 3.2 14.7 1.0 N A:HIS450 3.4 12.6 1.0 N A:ALA452 3.4 10.3 1.0 CB A:PRO449 3.6 11.3 1.0 O E:HOH189 3.7 18.5 1.0 CB A:VAL451 3.7 11.5 1.0 CA A:VAL451 3.7 10.0 1.0 CA A:PRO449 3.8 10.8 1.0 N3 D:DG406 3.9 13.1 1.0 C A:PRO449 3.9 11.6 1.0 ND1 A:HIS450 4.0 18.6 1.0 C2 D:DG406 4.0 10.9 1.0 CE1 A:HIS450 4.0 19.4 1.0 C A:HIS450 4.1 11.9 1.0 C A:VAL451 4.1 10.5 1.0 N3 E:DA429 4.2 14.0 1.0 CG2 A:VAL451 4.2 13.4 1.0 CB A:ALA452 4.3 11.1 1.0 CA A:HIS450 4.3 12.5 1.0 C2 E:DA429 4.3 14.1 1.0 CG A:HIS450 4.4 14.9 1.0 NE2 A:HIS450 4.4 17.7 1.0 CA A:ALA452 4.4 9.8 1.0 CD2 A:HIS450 4.6 18.1 1.0 CG A:PRO449 5.0 12.6 1.0 O A:PRO449 5.0 12.8 1.0 CB A:HIS450 5.0 15.1 1.0

Sodium binding site 2 out of 4 in the Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na634 b:9.6 occ:1.00 O F:HOH72 3.1 12.7 1.0 N B:VAL451 3.1 11.3 1.0 O C:HOH38 3.2 12.8 1.0 N2 C:DG406 3.3 12.8 1.0 N B:HIS450 3.4 11.4 1.0 N B:ALA452 3.5 9.2 1.0 CB B:VAL451 3.7 11.6 1.0 CB B:PRO449 3.7 10.4 1.0 O B:HOH65 3.8 14.5 1.0 CA B:VAL451 3.8 11.9 1.0 N3 C:DG406 3.9 10.5 1.0 CA B:PRO449 3.9 9.8 1.0 ND1 B:HIS450 4.0 16.4 1.0 C B:PRO449 4.0 9.4 1.0 CE1 B:HIS450 4.0 16.9 1.0 C2 C:DG406 4.0 11.4 1.0 C B:HIS450 4.1 11.3 1.0 C B:VAL451 4.2 9.8 1.0 N3 F:DA429 4.2 10.8 1.0 CG2 B:VAL451 4.2 12.1 1.0 CA B:HIS450 4.3 11.3 1.0 C2 F:DA429 4.3 12.8 1.0 CG B:HIS450 4.3 13.4 1.0 CB B:ALA452 4.4 9.3 1.0 NE2 B:HIS450 4.4 18.0 1.0 CA B:ALA452 4.5 9.1 1.0 CD2 B:HIS450 4.6 14.9 1.0 CB B:HIS450 4.9 13.2 1.0 O B:PRO449 5.0 12.0 1.0 CG1 B:VAL451 5.0 12.5 1.0

Sodium binding site 3 out of 4 in the Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na504 b:16.7 occ:1.00 O2 E:DT430 2.3 16.1 1.0 O D:HOH621 2.3 17.1 1.0 O2 D:EDO502 2.4 19.2 1.0 O2 E:EDO501 2.4 15.3 1.0 O1 D:EDO502 2.5 18.1 1.0 O4' E:DG431 2.6 14.2 1.0 C2 D:EDO502 3.3 21.4 1.0 C1 D:EDO502 3.3 21.9 1.0 C4' E:DG431 3.4 14.0 1.0 C2 E:EDO501 3.4 18.4 1.0 C2 E:DT430 3.5 14.8 1.0 C1' E:DG431 3.5 15.0 1.0 C1' E:DT430 3.9 15.4 1.0 N9 E:DG431 3.9 14.3 1.0 C5' E:DG431 4.1 12.2 1.0 O E:HOH189 4.2 18.5 1.0 N3 E:DG431 4.2 14.7 1.0 N1 E:DT430 4.2 14.1 1.0 C4 E:DG431 4.3 14.8 1.0 C2 D:DA404 4.3 13.8 1.0 C1 E:EDO501 4.3 19.8 1.0 O A:HOH87 4.4 17.0 1.0 O2 D:DT405 4.6 14.9 1.0 N3 E:DT430 4.6 16.1 1.0 C2' E:DT430 4.6 16.4 1.0 C3' E:DG431 4.7 12.8 1.0 C2' E:DG431 4.8 14.5 1.0 C8 E:DG431 4.9 15.9 1.0 O3' E:DG431 4.9 15.3 1.0 O A:HOH53 4.9 16.4 1.0 O E:HOH128 5.0 17.7 1.0 O5' E:DG431 5.0 12.2 1.0 O4' E:DT430 5.0 15.8 1.0 N1 D:DA404 5.0 15.3 1.0

Sodium binding site 4 out of 4 in the Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mouse UHRF1 Sra Domain Bound with Hemi-Methylated Cpg Dna, Crystal Structure in Space Group C222(1) at 1.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Na503 b:12.1 occ:1.00 O2 F:DT430 2.3 13.5 1.0 O C:HOH33 2.3 13.4 1.0 O2 F:EDO506 2.4 12.8 1.0 O1 C:EDO505 2.4 13.2 1.0 O2 C:EDO505 2.4 13.8 1.0 O4' F:DG431 2.6 11.5 1.0 C1 C:EDO505 3.2 16.3 1.0 C2 C:EDO505 3.3 14.6 1.0 C4' F:DG431 3.4 9.9 1.0 C2 F:EDO506 3.5 14.8 1.0 C2 F:DT430 3.5 11.5 1.0 C1' F:DG431 3.6 12.3 1.0 C1' F:DT430 4.0 12.0 1.0 C5' F:DG431 4.0 10.9 1.0 N9 F:DG431 4.1 12.7 1.0 N3 F:DG431 4.1 13.5 1.0 C1 F:EDO506 4.2 15.5 1.0 N1 F:DT430 4.2 10.6 1.0 C4 F:DG431 4.3 13.8 1.0 C2 C:DA404 4.3 11.5 1.0 O B:HOH65 4.4 14.5 1.0 O B:HOH51 4.5 13.3 1.0 N3 F:DT430 4.6 12.8 1.0 O2 C:DT405 4.6 12.1 1.0 C3' F:DG431 4.7 10.9 1.0 C2' F:DT430 4.7 12.8 1.0 O3' F:DG431 4.9 15.1 1.0 C2' F:DG431 4.9 12.4 1.0 O F:HOH59 4.9 14.4 1.0 O5' F:DG431 5.0 10.2 1.0 O1 F:EDO506 5.0 17.9 1.0

H.Hashimoto, J.R.Horton, X.Zhang, X.Cheng. UHRF1, A Modular Multi-Domain Protein, Regulates Replication-Coupled Crosstalk Between Dna Methylation and Histone Modifications. Epigenetics V. 4 8 2009.
ISSN: ISSN 1559-2294
PubMed: 19077538